# HG changeset patch
# User devteam
# Date 1478117571 14400
# Node ID 3a458e2680661144e512e3cb81ee2db1af82df2c
# Parent  06819360a9e2671e422403114df8cd97f2b34ce0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit 8918618a5ef7bdca55a31cd919efa593044a376e

diff -r 06819360a9e2 -r 3a458e268066 rgFastQC.py
--- a/rgFastQC.py	Mon Oct 31 10:40:12 2016 -0400
+++ b/rgFastQC.py	Wed Nov 02 16:12:51 2016 -0400
@@ -28,6 +28,7 @@
 import gzip
 import bz2
 import zipfile
+import mimetypes
 
 class FastQCRunner(object):
 
@@ -52,7 +53,8 @@
         trimext = False
         # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
         # patched may 29 2013 until this is fixed properly
-        if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
+        type = mimetypes.guess_type(self.opts.input)
+        if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip":
             f = gzip.open(self.opts.input)
             try:
                 f.readline()
@@ -95,8 +97,11 @@
 	    command_line.append('--limits %s' % opts.limits)
         command_line.append('--quiet')
         command_line.append('--extract') # to access the output text file
+	if type[-1] != "gzip":
+            command_line.append('-f %s' % opts.informat)
+	else:
+	    self.fastqinfilename += ".gz"
         command_line.append(self.fastqinfilename)
-        command_line.append('-f %s' % opts.informat)
         self.command_line = ' '.join(command_line)
 
     def copy_output_file_to_dataset(self):
diff -r 06819360a9e2 -r 3a458e268066 rgFastQC.xml
--- a/rgFastQC.xml	Mon Oct 31 10:40:12 2016 -0400
+++ b/rgFastQC.xml	Wed Nov 02 16:12:51 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="fastqc" name="FastQC" version="0.66">
+<tool id="fastqc" name="FastQC" version="0.67">
     <description>Read Quality reports</description>
     <requirements>
         <requirement type="package" version="0.11.5">fastqc</requirement>
@@ -48,6 +48,12 @@
             <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
             <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_file" value="1000gsample.fastq.gz" />
+            <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
+            <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
+        </test>
     </tests>
     <help>
 
@@ -63,7 +69,7 @@
 
 The main functions of FastQC are:
 
-- Import of data from BAM, SAM or FastQ files (any variant)
+- Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), 
 - Providing a quick overview to tell you in which areas there may be problems
 - Summary graphs and tables to quickly assess your data
 - Export of results to an HTML based permanent report
@@ -94,7 +100,7 @@
 FastQC_ is the best place to look for documentation - it's very good.
 A summary follows below for those in a tearing hurry.
 
-This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check.
+This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
 It will also take an optional file containing a list of contaminants information, in the form of
 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
diff -r 06819360a9e2 -r 3a458e268066 test-data/1000gsample.fastq.gz
Binary file test-data/1000gsample.fastq.gz has changed